Major Motoko Kusanagi from Ghost in the shell and Sniper wolf from Metal gear solid.
Playable character? Chell. The way I figure it I just want to play the game. I don’t want my character to express themselves because they’re guaranteed to be different than I am, and I’m there for the experience of the game, not the roleplaying aspect. I don’t care if my character doesn’t look like me, doesn’t sound like me, isn’t the same gender or ethnicity or anything else. I care if they open their mouth and say something I wouldn’t say in that situation. And that’s almost every vocalized character I’ve ever played as. Silence is golden.
Commenting on some of the previous mentions:
GLaDOS and SHODAN are honorable mentions for NPCs, but they’re both antagonists and AI (In universe), so they’re out on two counts. Both wonderful characters that were almost singlehandedly responsible for my enjoyment of their respective games.
Alyx Vance and Elizabeth from Bioshock Infinite were both pretty great as the actual lead characters of their games. (I feel the player was a supporting character more than the lead in both cases) Elizabeth’s leaning against walls and exploring the environment along with you really sold her as a companion and not a dumb NPC, though her “help” in battles got pretty irritating after awhile. Alyx was the first NPC follower that I didn’t just want to kill/trap ASAP and continue on without. Both did a wonderful job.
If I have to choose a favorite playable character with some level of personality, it’d be Lillith from Borderlands 1. But still, not for the personality, just for the abilities. Running around invincible, healing my allies and damaging enemies, while moving something like 1.25x to 1.5x as fast? That was fun. Until my friends banned me from playing that character because they thought it was so OP.
Ryoko from the Tenchi anime’s is my favorite. She’s wild, outrageous and sultry, yet she’s also sensitive, kind and caring. Plus, it doesn’t hurt that she’s the hottest chica I’ve ever laid eyes on.
Alyx Vance
Elizabeth
Miranda Lawson
Lara Croft
Catwoman
Not a protagonist but i really like Quinn from Batman Arkham City.
Samus all the way.
Boob armors and anachronistic silicone, is tacky 
I had intentionally left my question somewhat vague or open-ended so that I could get a wider response; I’m mostly interested in the “why’s” of what people pick. So I’m not too opposed to people mentioning non-playable characters, but I must admit I am surprised at how many non-playable’s wound up being mentioned.
Thank you all for these informative responses.
To be fair I think a lot of my favorite male characters would end up NPCs as well. Probably more favorite playable characters on the male side though.
Female characters in games usually suffer the same fate as female characters, in books written by male writers (who aren’t exceptional).
Venus and mars, etc. Most men (writers) simply can’t grasp the female mind.
Not that I think I have a better understanding of the inner workings of the other 52% of the population:p
The latest Lara Croft and Elizabeth from BioShock Infinite are outstanding!
I think that fact is made doubley-potent in video games. While there are a few exceptions, video games are almost unanimously about conflict. And not an emotional conflict like you have in some books and movies, but physical conflict. You need to save the world. You do this by fighting. You need to kill all the bad-guys. If a game has characters, (ie, not some matching puzzle game,) then it’s about 99.55% likely to be about killing/defeating someone.
It’s not exactly an environment geared toward natural feminine tendencies. So even when we have women in leading roles in a game, they kind of need to adopt masculine traits.
So I think this thread is about imaging gender in games, asking specifically about women.
My guess is heterosexual men want to play as what they desire to be or how they would like te be seen; strong, cool and winning. And they want the opposite gender to behave in a role ideal according to their superficial needs. And that superficial role is quite flat. So that is seen commonly in fiction made by men, as in western culture males were dominant for many millenias. The picture that is generated by that history is still prevalent and gets copied all over, because that is easy and you have lots of examples to build up upon.
Im happy when my male char pictures someone I’d like to go out with. And female chars, especially those that play that flat rolemodel for the majority of men as described above, are just an annoyance.
Interesting would be if women have the same view of the world, just inverted; if they try to look beyond the cultural habbits. My guess is, its just that. They want to play as a female character that’s strong, cool and winning, and the men roles to just behave to their needs; that is equally flat as above, just inverted.
And I think cultural output drifts towards this reality, men, women, straight and gay, all in equally mixed in switching roles so that every party can have their expectations met without insulting the self-picture of the other sides. Just as a random example the crew of Warehouse 13. Or Torchwood. Lots of others. If game makers get around to construct those roles in their games, that leads to ‘game gender riots’ as my news site tells me exists in the US loose all needs for existence. And I think there are a some really good games doing that really successfully, as random example Mass Effect.
I dont believe in the existence of any natural tendencies that are fundamentally different between men and women ( I don’t talk about the ability to give birth or bend steel :p, I talk about the mind). Women fight well in wars, women are competing hard with each other, women have bright minds in science, women play shooters, whatnot else. It’s just some facets of beeing men or women or whatnot are superficially hidden from ones view because one has no interest in their existence.
Maybe some female forum member sheds light of what she thinks about this 
For Me Kratos from God Of War 
Ellie from The Last of Us
Either Elh or Chocolat from Solatorobo.
Followed by Cortana and Clementine, from Halo and TWD (respectively).